ec18dd438e8210ae0706f614f7bf39eb *DESCRIPTION
040b37f08946cea72b179083d6406ed9 *NAMESPACE
5d4b69856a24694aa256a572f6a8bed3 *R/are_beast2_input_lines.R
6dfd14b839853a44095c149cde9e5eea *R/beastier.R
788c03d16609713a3cccda05b387e008 *R/check_beast2.R
ed70ad5fb2ecafe715b2b9f673d968fb *R/check_beast2_options.R
0ec48d85b694c2b086d7f08889800725 *R/check_beast2_optionses.R
4a35bf3af1d6b4e96cc62b3bbf1de52b *R/check_beast2_path.R
7c23ad1ecd3ff4109ad6347ffdf1d73c *R/check_input_filename.R
197d62ba1e6ee65918d5f2ba32620143 *R/check_n_threads.R
603f5787f4392dbe42223a72338c6c3c *R/check_os.R
5826398039227d682bb79417ee181bdc *R/check_rng_seed.R
c7c63aa9ab566be5517d502d6a12f76b *R/create_beast2_options.R
0e8d48b55efc1aec479946086422085a *R/create_beast2_run_cmd.R
ba6b420a91f82dcbb9a171ba2c2fd368 *R/create_beast2_validate_cmd.R
f52fe2e05166bc6ebb96a451f4a91a45 *R/create_default_log_filename.R
c7e0c3636788eaadaf8d5a6b1710c974 *R/create_default_trees_filename.R
f1e89d87f62010757745ac7f9604c0b0 *R/create_random_alignment.R
599bcd33935927fad1f9beb9c71ea036 *R/create_random_fasta.R
28c15f484b3876c99eb7c0a0c800ae0c *R/create_random_phylogeny.R
552148069e3e878366b1f2fca9d0762a *R/default_params_doc.R
05d0c21659de5466cc1b7d5d6c3b93f7 *R/do_minimal_run.R
0ffcb3a5caf97a8f900de004387522ce *R/files_exist.R
8140307141a52a8b69c65391f16e9eff *R/get_alignment_ids.R
78a650c2263a5de682c67ef93157a68e *R/get_default_beast2_bin_path.R
d6235be6ab09d37e64628a03caf61596 *R/get_default_beast2_download_url.R
a2e617ab0dae7dbd6a8e68cd900a6c5c *R/get_default_beast2_folder.R
8b64c529f3cc763e3b91bf8d4ad87d29 *R/get_default_beast2_jar_path.R
14218030d7b436c10b5e3179c7efe099 *R/get_default_beast2_path.R
7ddf32b9b6d6c08f630c1ade35ea0468 *R/get_default_java_path.R
21315d90d42ef2609a83ae9261ce3049 *R/get_duplicate_param_ids.R
4660761297b2179b0c2d8545def67b50 *R/get_path.R
1ff1fa6e1ca737529d14a13e309703a8 *R/get_paths.R
0dce41b4b5c98ff9fefbdda0a59d77da *R/get_trees_filenames.R
4b72eab02c7a4260ec198a18fa279cdd *R/gives_beast2_warning.R
896a781565738d245b61bd901462dc1c *R/has_unique_ids.R
e909bf4862fa77f76ec33756e53d66aa *R/install_beast2.R
bb21401b702dffb4b71c7be0d8a6b0be *R/is_beast2_input_file.R
6d657273eb4fc90b624abd212725e67d *R/is_beast2_installed.R
273bffa319255ab1b22311ddc9261093 *R/is_bin_path.R
33963423914dd7907961f21467a1da13 *R/is_jar_path.R
a9acc7076e6ec73c01c675e46c1212c0 *R/is_on_ci.R
e7eab266c37c94891e4c645cc5a15b1d *R/run_beast2.R
454832d66cc60145d207c62eb93cd939 *R/run_beast2_from_options.R
9a51384dbbc5d73582b69ac49293065d *R/save_lines.R
3289fa19b4c4743a97ffd0b8605cd620 *R/uninstall_beast2.R
0c840aa887ee0710b8c655fff1bd8252 *build/vignette.rds
604d69ff7d5954219736e01c41d18e48 *inst/CITATION
d3de91ee271160e57084af0a4c7ffcda *inst/WORDLIST
6f5fd1975c9189de2fd0d72b3d3b625e *inst/doc/demo.R
3c9409d15f1e7356003bd81aa52a7841 *inst/doc/demo.Rmd
067190d0b0a137f05ff0cc02723c4f43 *inst/doc/demo.html
59dc5020cc76a70d138c1465d93c5b12 *inst/extdata/2_4.xml
0f10b2e8a0c32ae1593678977e71d909 *inst/extdata/anthus_15_15.xml
e448411f3b6ecbf4d2304a23fabcb788 *inst/extdata/anthus_15_15_long.xml
a5b87ff2e286d857fa94735b096f69e4 *inst/extdata/anthus_15_26.xml
ff3ce7acb6c88f7c8cbedce5274f64a5 *inst/extdata/anthus_15_na.xml
a75c01a5ea48922948f932b39597be48 *inst/extdata/anthus_2_4.xml
0eedfd95a1fff834d513246b4e4624e2 *inst/extdata/anthus_aco.fas
e39a06790872a8429c306e0d0ac4a080 *inst/extdata/anthus_na_15.xml
4f47d3dda06c4ad6605b84cf43579113 *inst/extdata/anthus_na_na.xml
93d45a2f0c0145ebfebdedeb073025f1 *inst/extdata/anthus_nd2.fas
b8231c2de96de5d0c4ab0082a38c41d5 *inst/extdata/beast2_example_output.log
f83191933040361f729577af64c44110 *inst/extdata/beast2_example_output.trees
346226afa164793704af01106aa3b2d8 *inst/extdata/beast2_example_output.xml
5ac7281e62e96d3c330bb6072aa6096d *inst/extdata/beast2_example_output.xml.state
f175cffff0c68f238ea16652fe6456ea *inst/extdata/beast2_warning.xml
4ce27062dcd961771b12dd9adfcdd946 *inst/extdata/nested_sampling.xml
b2681db80ca3445eea3fcb15dff6124a *inst/extdata/read_beast2_trees_example.trees
cf67cea70b8b6fa59bbd3c07995c052f *man/are_beast2_input_lines.Rd
a1aa411479f0306eb9071bb25ebfaa94 *man/are_beast2_input_lines_deep.Rd
0bc2098cd8c7485f1f237c12a66c8284 *man/are_beast2_input_lines_fast.Rd
536d13f5ffd054887f962856303c2f25 *man/beastier.Rd
02e6a6eb2f6d720ed137c287ca8f7275 *man/check_beast2.Rd
6aa11b94dde59476c47aa4849f13a2d5 *man/check_beast2_options.Rd
390d3c3a824465d85891407f15523ace *man/check_beast2_optionses.Rd
c265634dd0e57879bdf8052662dd806e *man/check_beast2_path.Rd
c943a980baecb29603aba6df9efbe859 *man/check_input_filename.Rd
dea892717a8a523e4adf9ab1eab4321a *man/check_n_threads.Rd
f6ef1cba350f5dd5f2285b5023ce89b1 *man/check_os.Rd
ddc1d95368965611911f3bff725a87c8 *man/check_rng_seed.Rd
eed1f32205f3df13071ac0d89c495e5a *man/create_beast2_options.Rd
20121f0cc968b56ee4ef99d39a4b73b3 *man/create_beast2_run_cmd.Rd
17c56f221aa81b558021f8d844af2b1f *man/create_beast2_validate_cmd.Rd
505bb9c7408815cb880131fa4fd55e5a *man/create_beast2_validate_cmd_bin.Rd
b6ac0126053a22804e07ba53cecfbf9a *man/create_beast2_validate_cmd_jar.Rd
7f8067e31f29bf839333a557b2259457 *man/create_default_log_filename.Rd
eed177e7d6182fbec815125b5eae9edb *man/create_default_trees_filenames.Rd
cb6771e4101af2f2281ff61e778ddbd6 *man/default_params_doc.Rd
f02302076caf6574d44ca9f34e9a7a2b *man/do_minimal_run.Rd
ca726ca2a8e5add53f926e33cc8313cc *man/files_exist.Rd
522335a740b68a692cb43accd2eb34e0 *man/get_alignment_ids.Rd
700960db63ab1aed428eeb0b2102f30d *man/get_beastier_path.Rd
001de36b02bdddc4f07686531e5b22ce *man/get_beastier_paths.Rd
18f11cf58a374f463e0ca0472cb7f2d3 *man/get_default_beast2_bin_path.Rd
610bfb7738454cf59d34a89dd7d75f0c *man/get_default_beast2_folder.Rd
df3ca538d57a7efbe3b6ae435118fc3c *man/get_default_beast2_jar_path.Rd
146c4b1b89db541c72a11f1730df30d5 *man/get_default_beast2_path.Rd
8a2d89c99fcea1f70f201fb7a5c3fa04 *man/get_default_java_path.Rd
06da65ca4ef028106830d77e9fe6f026 *man/get_trees_filenames.Rd
7faa09d7eb67d6554917c8ea55d0bd4e *man/gives_beast2_warning.Rd
3b0fd58c6f1dac6fda10f284433ea20a *man/install_beast2.Rd
39d978a00e273e65bc31cab1bb797c65 *man/is_beast2_input_file.Rd
61edfc984b5db000f926df37ea20ad6d *man/is_beast2_installed.Rd
3cf8c2f3c47a9504ab5c18a701db8c80 *man/is_bin_path.Rd
b428bc38d93cc19e9e1f2b95a868ce18 *man/is_on_appveyor.Rd
1a6e9b7e9ff758f9ec39798eb0ac26b7 *man/is_on_ci.Rd
1bd58c528cd6ae013e927953fd44e41d *man/is_on_travis.Rd
57e71ce491d70c0197bb7a68e8e8b891 *man/run_beast2.Rd
a80672fd72b76aa408b9a7b1458e9935 *man/run_beast2_from_options.Rd
a6d2b74d416436de5633d054cd6d5ca4 *man/uninstall_beast2.Rd
3c9409d15f1e7356003bd81aa52a7841 *vignettes/demo.Rmd
